A universal simulator for ecological models

Ecological Informatics

Volumn 13, Issue , 2013, Pages 70-76

  Holst, Niels ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Agile; C++; Object oriented; Simulation model; Software design; XML

Indexed keywords

DESIGN; ECOLOGICAL MODELING; NUMERICAL MODEL; SOFTWARE; THEORETICAL STUDY;

EID: 84870821845     PISSN: 15749541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecoinf.2012.11.001     Document Type: Article

References (35)

1. Bar M., Fogel K. Open Source Development with CVS 2003, Paraglyph Press, Scottsdale, Arizona. third ed.
2. Beck K. Test Driven Development: By Example 2002, Addison-Wesley, Boston.
3. Bray T., Paoli J., Sperberg-McQuenn C.M., Maler E., Yeargeau F. Extensible Markup Language (XML) 1.0 2008, (www.w3.org, 18 May 2012).
4. Chacon S. Pro Git 2009, Apress, Inc., New York.
5. Clark J., DeRose S. XML Path Language (XPath) 1999, (Version 1.0. www.w3.org, 18 May 2012).
6. Gamma E., Helm R., Johnson R., Vlissides J. Design Patterns. Elements of Reusable Object-oriented Software 1995, Addison-Wesley Publishing Company, Reading, Massachusetts.
7. Gutierrez A.P., Baumgärtner J.U. II. A realistic model of plant-herbivore-parasitoid-predator interactions. Canadian Entomologist 1984, 116:933-949.
8. Hillyer C., Bolte J., van Evert F., Lamaker A. The ModCom modular simulation system. European Journal of Agronomy 2003, 333-343.
9. Holst N. WeedML: a tool for collaborative weed demographic modeling. Weed Science 2010, 58:497-502.
10. Holzworth D., Huth N., de Voil P. A framework independent component design: keeping it simple. Proceedings of the International Congress on Modelling and Simulation, 10-13 September 2007 2007, 1138-1144. University of Western Australia, Nedlands, Virginia Beach, Virginia.
11. Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor V., Goryanin I.I., Hedley W.J., Hodgman T.C., Hofmeyr J.H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novere N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531.
12. Krivov S., Dahiya A., Ashraf J. From equations to patterns: logic-based approach to general systems theory. International Journal of General Systems 2010, 31:183-205.
13. Larkin T.S., Carruthers R.I. Development of a hierarchical simulation environment for research biologists. Object Oriented Simulation 1989, 49-54. Society for Computer Simulation, San Diego, California. A. Gausch (Ed.).
14. Marsh J., Orchard D., Veillard D. XML Inclusions (XInclude) 2006, (Version 1.0 www.w3.org, 18 May 2012).
15. Martin R.C. Agile Software Development: Principles, Patterns, and Practices 2006, Prentice-Hall, Upper Saddle River, New Jersey.
16. Martin R.C. Clean code. A Handbook of Agile Software Craftsmanship 2009, Prentice-Hall, Upper Saddle River, New Jersey.
17. Moore A.D., Holzworth D.P., Herrmann N.I., Huth N.I., Robertson M.J. The Common Modelling Protocol: a hierarchical framework for simulation of agricultural and environmental systems. Agricultural Systems 2007, 95:37-48.
18. Papajorgji P., Beck H.W., Braga J.L. An architecture for developing service-oriented and component-based environmental models. Ecological Modelling 2004, 179:61-76.
19. Parnas D.L., Clements P.C. A rational design process: how and why to fake it. IEEE Transactions on Software Engineering 1986, SE-12:251-257.
20. Parr T. Language Implementation Patterns: Create Your Own Domain-specific and General Programming Languages 2009, The Pragmatic Bookshelf, Dallas, Texas.
21. R Development Core Team R: A Language and Environment for Statistical Computing 2011, R Foundation for Statistical Computing, Vienna, Austria.
22. Reynolds J.F., Acock B. Modularity and genericness in plant and ecosystem models. Ecological Modelling 1997, 94:7-16.
23. Robertson D., Bundy A., Uschold M., Muetzelfeldt R. The ECO program construction system: ways of increasing its representational power and their effects on the user interface. International Journal of Man-Machine Studies 1989, 31:1-26.
24. Saltelli A., Ratto M., Andres T., Campolongo F., Cariboni J., Gatelli D., Saisana M., Tarantola S. Global Sensitivity Analysis 2008, John Wiley & Sons, Ltd., Chichester, England.
25. Silvert W. Object-oriented ecosystem modeling. Ecological Modelling 1993, 68:91-118.
26. Stubben C.J., Milligan B.G. Estimating and analyzing demographic models using the popbio package in R. Journal of Statistical Software 2007, 22.
27. Tisue S., Wilensky U. NetLogo: design and implementation of a multi-agent modeling environment. Proceedings of SwarmFest 2004, Ann Arbor, 9-11 May 2004 2004, University of Michigan, Ann Arbor.
28. Topping C.J., Høye T.T., Olesen C.R. Opening the black box-development, testing and documentation of a mechanistically rich agent-based model. Ecological Modelling 2010, 221:245-255.
29. Uso-Domenech J.L., Vives-Macia F., Mateu J. Regular grammars of L(M-T): a language for ecological systems modelling (II). Kybernetes 2006, 35:1636-1645.
30. Villa F. Integrating modelling architecture: a declarative framework for multi-paradigm, multi-scale ecological modelling. Ecological Modelling 2001, 137:23-43.
31. Villa F., Athanasiadis I., Rizzoli A.E. Modelling with knowledge: a review of emerging semantic approaches to environmental modelling. Environmental Modelling and Software 2009, 24:577-587. (N.).
32. Voinov A., Fitz C., Boumans R., Costanza R. Modular ecosystem modeling. Environmental Modelling and Software 2004, 19:285-304.
33. Vose D. Risk Analysis: A Quantitative Guide 2000, John Wiley & Sons, Ltd., Chichester, UK.
34. Wenzel F. Semantics and syntax elements and a unique calculus for modelling of complex ecological systems. Ecological Modelling 1992, 63:113-131.
35. Wittgenstein L. Tractatus Logico-Philosophicus 1922, Harcourt, Brace and Co., Inc., New York.